One side is happy. The other side, well, not so much. It’s a case where shades of gray are hard to find.

That’s the fallout following a decision by Mayor Jerry Sanders last month to endorse a continued conditional-use permit issued to the Rock Church megachurch in Liberty Station in 2004.

Sanders rejected a recommendation by the San Diego County Grand Jury that opined the 3,500-seat church did not belong in Liberty Station primarily because of traffic and parking concerns and incompatibility with local land-use plans. The grand jury recommended that the city suspend the Rock Church’s permit — a recommendation that was subsequently supported by a majority of the Peninsula Community Planning Board (PCPB) in July.

The grand jury recommendation, if it had been supported by Sanders, could have meant canceling the five services the church schedules every Sunday for its 12,000-plus members, as well as turning away the 400-plus students from pre-kindergarden to high school who attend the Rock Church Academy during the week, while the city reviewed whether the church’s permit was mistakenly issued in the first place, as detractors claim.

“We’re very pleased, but not surprised, with the city’s response to the grand jury report,” said Mark Stevens, the church’s chief operating officer, in a mass email to congregation members following the mayor’s response.

Others were clearly unhappy with Sanders’ decision.

“It’s unfortunate. It’s really unpleasant for [the church’s neighbors],” said Bonnie Mann, who lives near the church and is also a plaintiff in a lawsuit against the Corky McMillin Companies, developer of the 349 homes at Liberty Station. The lawsuit alleges information about the Rock Church and its potential impacts was concealed from prospective homebuyers during the time the original permit was approved.

The grand jury in May made a finding that the church was not a compatible land use because the Liberty Station Precise Plan called for the area surrounding the church to be devoted to educational uses.

In addition, the grand jury report states, “Traffic congestion, parking problems, [and] the need for a street closure … are directly related to a church not being compatible for the Liberty Station area.”

But in an Aug. 22 letter to Robert J. Trentacosta, presiding judge of the San Diego Superior Court, Sanders said he disagreed with the grand jury, saying its recommendations were “not warranted or reasonable.”

Sanders said the area’s precise plan is only a “policy document to guide redevelopment at Liberty Station” and pointed out that a church is allowable with a conditional-use permit under the site’s commercial zone.

He also said church activities were not necessarily the cause of traffic congestion, street closures and parking problems on Sundays.

“[T]here are many other commercial, retail, park and special-event uses, which also typically are operating at Liberty Station during this timeframe,” Sanders states in his letter.

Mann disagreed.

“The mayor says a church is appropriate,” she said. “But this is no typical church. This is clearly a megachurch.”

Most churches with large congregations have a much larger footprint, are located in an outlying area and control their own parking — characteristics the Rock Church lacks, Mann said.

“The church is too big for this confined area,” she said.

Even though the church prevailed, the divisive scenario is a bit of a wake-up call, Stevens acknowledged in his email to church members.

“[T]he situation is a reminder that we need to continue to uphold the standards we have set for our staff and congregation to be good neighbors,” he said.

Geoff Page, who chairs the Peninsula Community Planning Board, said there are no plans to formally respond to the mayor’s decision, although that could change.